This gene encodes a filamentous-actin-associated protein, which is involved in actin dynamics and plays an important role in neuromorphogenesis. This protein is part of the KICSTOR protein complex that localizes to lysosomes. Mutations in this gene result in an autosomal recessive form of intellectual disability. Alternatively spliced transcript variants have been found for this gene. [provided by RefSeq, Jul 2017]
Transcription factors with Perturb-seq knockdown data for KPTN. The Binding column indicates whether any binding evidence exists for this TF–gene pair (ChIP-seq or motif footprint peaks). The Mean coef is the average Perturb-seq regression coefficient across active gRNAs (positive = KPTN upregulated upon KD; negative = downregulated). The Outlier column indicates whether this gene is in the top or bottom 5% of all TF knockdown effects.
| TF | Mean coef | Binding | Outlier | TF→Gene link |
|---|
Open chromatin peaks (ATAC-seq) in the genomic neighbourhood of KPTN, linked by TSS proximity or chromatin conformation (Multiome / HiCAR). Each element overlaps at least one TF ChIP-seq binding site — the TFs column shows how many distinct TFs bind that element.
| Accessibility | Element | Dist. to TSS | Link type | TFs |
|---|---|---|---|---|
| chr19:45,632,406–45,633,148 | 1851.5 kb | Distal (>10kb) Multiome HiCAR | 358 | |
| chr19:45,638,965–45,639,696 | 1844.9 kb | Distal (>10kb) Multiome HiCAR | 477 | |
| chr19:47,196,586–47,197,452 | 287.4 kb | Distal (>10kb) Multiome | 94 | |
| chr19:47,225,386–47,231,990 | 256.4 kb | Distal (>10kb) Multiome | 1389 | |
| chr19:47,240,827–47,241,572 | 243.0 kb | Distal (>10kb) Multiome | 616 | |
| chr19:47,242,713–47,243,645 | 241.1 kb | Distal (>10kb) Multiome | 568 | |
| chr19:47,243,835–47,244,896 | 239.9 kb | Distal (>10kb) Multiome | 1001 | |
| chr19:47,256,041–47,258,057 | 227.1 kb | Distal (>10kb) Multiome | 907 | |
| chr19:47,272,778–47,275,890 | 210.8 kb | Distal (>10kb) Multiome | 931 | |
| chr19:47,348,695–47,349,758 | 135.0 kb | Distal (>10kb) Multiome | 766 | |
| chr19:47,406,825–47,407,408 | 76.9 kb | Distal (>10kb) Multiome | 333 | |
| chr19:47,427,132–47,428,809 | 57.0 kb | Distal (>10kb) Multiome | 506 | |
| chr19:47,429,865–47,430,531 | 53.9 kb | Distal (>10kb) Multiome | 438 | |
| chr19:47,447,043–47,448,262 | 36.6 kb | Distal (>10kb) Multiome | 510 | |
| chr19:47,471,631–47,472,340 | 12.2 kb | Distal (>10kb) Multiome | 500 | |
| chr19:47,479,940–47,480,772 | 4.1 kb | Proximal (<10kb) Multiome | 147 | |
| chr19:47,483,636–47,484,543 | 47 bp | At TSS Multiome | 841 | |
| chr19:47,514,152–47,515,901 | 31.1 kb | Distal (>10kb) Multiome | 895 | |
| chr19:47,600,223–47,600,983 | 116.3 kb | Distal (>10kb) Multiome | 807 | |
| chr19:47,607,980–47,609,479 | 124.6 kb | Distal (>10kb) Multiome | 832 | |
| chr19:47,647,803–47,648,987 | 164.2 kb | Distal (>10kb) Multiome | 693 | |
| chr19:47,697,956–47,698,391 | 214.0 kb | Distal (>10kb) Multiome HiCAR | 453 | |
| chr19:47,729,949–47,730,505 | 246.0 kb | Distal (>10kb) Multiome | 425 | |
| chr19:47,743,369–47,743,911 | 259.5 kb | Distal (>10kb) Multiome | 929 | |
| chr19:47,745,136–47,745,915 | 261.4 kb | Distal (>10kb) Multiome | 784 | |
| chr19:47,765,762–47,766,380 | 281.8 kb | Distal (>10kb) Multiome | 296 | |
| chr19:47,770,120–47,770,789 | 286.2 kb | Distal (>10kb) Multiome | 127 | |
| chr19:47,778,102–47,779,241 | 294.3 kb | Distal (>10kb) Multiome | 845 | |
| chr19:48,363,062–48,364,710 | 880.1 kb | Distal (>10kb) Multiome HiCAR | 940 |
Genomic view of the KPTN locus showing ATAC-seq accessibility and RNA-seq expression across the ESC → DE time course, together with TF binding peaks and element-to-TSS loop connections.